Question: Annotations for Affymetrix HT HG-U133+ PM Array Plate
1
gravatar for giroudpaul
4 months ago by
giroudpaul70
European Union
giroudpaul70 wrote:

Hi,

I am trying to analyze a GSE that was performed on affymetrix HT HG-U133+ PM Array Plate GPL13158

But I cannot find the corresponding annotation package on bioconductor.

Affymetrix website is of no use, return a 404 error when selecting the array.

If anyone has experience with this array and know how to map gene name to probe name, I would be glad to have some help

Thanks

R affimetrix • 164 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe56k • written 4 months ago by giroudpaul70
2
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

Oh yeh, some of those links to Affymetrix pages will be broken due to [I believe] the merger between ThermoFisher and Affymetrix. You can now find technical information on either or both websites, like, for example: HT HG-U133+ PM Array Plate - Support Materials.

The HT_HG-U133_Plus_PM is merely a modified version of the original U133 - it has no mismatch (MM) probes and has a few other modifications.

There is a Bioconductor package HERE. You may have to install it from the source tar.gz.

If not the Bioconductor package, then just download the annotation table at the bottom of the GEO page (GPL13158), and load that manually into the fdata slot of the ExpressionSet object.

Kevin

ADD COMMENTlink written 4 months ago by Kevin Blighe56k
1

Thank you for your answer,

I see you indicated me the AffyGenePDInfo, and I was not finding anything because I search for the ChipDB package, which does not exist.

I did not manage to annotate my data using it though, I tried with affycoretools::annotateEset, but I get the following error : "There is no annotation object provided with the x package." which I do not understand.

So I will try to use the annotation table from GEO, which I though would be my last resort. Hope I can get it to work this way !

ADD REPLYlink written 3 months ago by giroudpaul70
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